Water, Sanitation and Hygiene (WASH) programs in schools can increase the health, dignity and comfort of students and teachers. Understanding the costs of WASH facilities and services in schools is one essential piece for policy makers to utilize when budgeting for schools and helping to make WASH programs more sustainable. In this study we collected data from NGO and government offices, local hardware shops and 89 rural primary schools across three Kenyan counties. Current expenditures on WASH, from school and external (NGO, government, parent) sources, averaged 1.83 USD per student per year. After reviewing current expenditures, estimated costs of operations and maintenance for bringing schools up to basic WASH standards, were calculated to be 3.03 USD per student per year. This includes recurrent costs, but not the cost of installing or setting up WASH infrastructure, which was 18,916 USD per school, for a school of 400 students (4.92 USD per student, per year). These findings demonstrate the need for increases in allocations to schools in Kenya, and stricter guidance on how money should be spent on WASH inputs to enable all schools to provide basic WASH for all students.